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Gao C, Che B, Dai H. A new G-triplex-based strategy for sensitivity enhancement of the detection of endonuclease activity and inhibition. RSC Adv 2021; 11:28008-28013. [PMID: 35480740 PMCID: PMC9037997 DOI: 10.1039/d1ra04203c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/14/2021] [Indexed: 01/09/2023] Open
Abstract
EcoRI is an important biomacromolecule in live cells and protects bacterial cells against foreign DNA. In this work, we developed a simple and convenient G-triplex (G3) (5′-TGGGAAGGGAGGGAATTCCCT-3′)-based colorimetric assay for the rapid and selective detection of EcoRI activity and inhibition. The sequence specifically responds to EcoRI in the presence of K+ and hemin to form a G-triplex/hemin complex. Taking advantage of G-triplex, EcoRI activity was investigated under the optimized conditions. The absorption intensity ratio displayed a linear relationship against the concentration of EcoRI in the range 0 to 100 U mL−1, and the detection limit was 5.7 U mL−1. Furthermore, G3 showed good selectivity, and the ability to be used to screen for EcoRI inhibitors, indicating its potential in detection and analysis applications. A new G-triplex-based probe was developed for detecting EcoRI activity and inhibition. The probe showed good selectivity towards EcoRI. The assay was colorimetric and can be monitored by the naked eye.![]()
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Affiliation(s)
- Congcong Gao
- Beijing Institute for Drug Control, MNPA Key Laboratory for Quality Evaluation of Traditional Chinese Medicine (Traditional Chinese Medicine), MNPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing Key Laboratory of Analysis and Evaluation on Chinese Medicine Beijing 102206 China
| | - Baoquan Che
- Beijing Institute for Drug Control, MNPA Key Laboratory for Quality Evaluation of Traditional Chinese Medicine (Traditional Chinese Medicine), MNPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing Key Laboratory of Analysis and Evaluation on Chinese Medicine Beijing 102206 China
| | - Hong Dai
- Beijing Institute for Drug Control, MNPA Key Laboratory for Quality Evaluation of Traditional Chinese Medicine (Traditional Chinese Medicine), MNPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing Key Laboratory of Analysis and Evaluation on Chinese Medicine Beijing 102206 China
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2
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Chen ZP, Zhang HM, Yang P, Yuan R, Li Y, Liang WB. No-nonspecific recognition-based amplification strategy for endonuclease activity screening with dual-color DNA nano-clew. Biosens Bioelectron 2021; 190:113446. [PMID: 34166945 DOI: 10.1016/j.bios.2021.113446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 10/21/2022]
Abstract
The inevitable nonspecific recognition severely restricted widely used nucleic acid amplification strategies, which has become an urgent problem in current scientific research. Herein, we developed a novel no-nonspecific recognition-based amplification strategy to construct dual-color dye loaded nano-clew as ultrabright illuminant for screening endonuclease activity with Escherichia coliRY13 I (EcoR I) as a model, which overcame some major drawbacks such as nonspecific recognition and photobleaching. Typically, the target endonuclease induces cleavage of the customized dumbbell-shape substrate (DSS) to generate two same triggers that can initiate the rolling circle amplification (RCA) to prepare long single-strand DNA (lssDNA), which could self-assemble into irregular DNA nano-clew based on the electrostatic interactions with Mg2+ to furtherly capture the donor and accepter fluorophore proximately, constructing the dye loaded nano-clew with dual-color fluorescence (FL) emission to resist photobleaching. Importantly, in absence of EcoR I, even if the DSS could combine with circular template a little, the reaction system performed hardly RCA reaction due to no cohesive terminus, resulting an extremely low background fluorescence signal because of the prevention of nonspecific RCA reaction. As expected, the proposed sensing platform with a low limit of detection (LOD) of 3.4 × 10-7 U/μL was demonstrated to work well for endonuclease inhibitors screening also. Furthermore, the proposed no-nonspecific recognition strategy could be readily extended to various DNA or RNA enzymes such as DNA methyltransferase, DNA repair-related enzymes and polynucleotide kinase just by simply changing the recognition sequence in the DNA substrate, performing great potential of endonucleases-related clinical diagnosis and drugs discovery.
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Affiliation(s)
- Zhao-Peng Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Hao-Min Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Peng Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Yan Li
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China.
| | - Wen-Bin Liang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China.
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3
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Tao G, Xu X, Li RS, Liu F, Li N. Nonamplification Multiplexed Assay of Endonucleases and DNA Methyltransferases by Colocalized Particle Counting. ACS Sens 2021; 6:1321-1329. [PMID: 33496573 DOI: 10.1021/acssensors.0c02665] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Restriction endonucleases (ENases) and DNA methyltransferases (MTases) are important enzymes in biological processes, and detection of ENases/MTases activity is significant for biological and pharmaceutical studies. However, available nonamplification methods with a versatile design, desirable sensitivity, and signal production mode of unbiased quantification toward multiple nucleases are rare. By combining deliberately designed hairpin DNA probes with the colocalized particle counting technique, we present a nonamplification, separation-free method for multiplexed detection of ENases and MTases. In the presence of target ENases, the hairpin DNA is cleaved and the resulting DNA sequence forms a sandwich structure to tie two different-colored fluorescent microbeads together to generate a colocalization signal that can be easily detected using a standard fluorescence microscope. The multiplexed assay is realized via different color combinations. For the assay of methyltransferase, methylation by MTases prevents cleavage of the hairpin by the corresponding ENase, leading to decreased colocalization events. Three ENases can be simultaneously detected with high selectivity, minimal cross-talk, and detection limits of (4.1-6.4) × 10-4 U/mL, and the corresponding MTase activity can be measured without a change of the probe design. The potential for practical application is evaluated with human serum samples and different ENase and MTase inhibitors with satisfactory results. The proposed method is separation-free, unbiased toward multiple targets, and easy to implement, and the strategy has the potential to be extended to other targets.
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Affiliation(s)
- Guangyu Tao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiao Xu
- Environmental Metrology Center, National Institute of Metrology, Beijing 100029, China
| | - Rong Sheng Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Feng Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Na Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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4
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Tang Z, Liu H, Chen M, Ma C. Label-free one-step fluorescent method for the detection of endonuclease activity based on thioflavin T/G-quadruplex. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117823. [PMID: 31767417 DOI: 10.1016/j.saa.2019.117823] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/06/2019] [Accepted: 11/18/2019] [Indexed: 06/10/2023]
Abstract
Endonucleases, one of the basic tool enzymes of modern molecular biology and medical genetics, have also been clarified as the potential targets for antimicrobial and antiviral drugs screening. However, traditional assays to monitor endonuclease activity can be expensive, time-consuming, or laborious. In order to provide new detective platform, we proposed a novel label-free one-step fluorescent method for the detection of endonuclease activity based on cleavage-induced G-quadruplex formation. In this detection system, a simple DNA probe can spontaneously form a duplex structure with recognition sites of EcoRI and prevent the generation of the G-quadruplex. Once EcoRI is present, the recognition sites in the duplex DNA are cleavage, producing a free guanine-rich sequence to form G-quadruplex. When thioflavin T (ThT) is added, a strong fluorescence signal is given by ThT/G-quadruplex, and therefore the EcoRI activity can be detected. After systematic investigation and optimization, this method has gained a sensitive limit of detection at 0.75 U/mL, and a wide detection range between 0.75 U/mL and 120 U/mL. Furthermore, the inhibitory effect of 5-fluorouracil on EcoRI activity was verified and IC50 was calculated. Taken together, these experimental results have proven that this turn-on fluorescent method has considerable analytical performances. As far as we are concerned, this method is the first reported EcoRI assay based on ThT/G-quadruplex, and only one kind of probe and one kind of dye are involved, providing one of the simplest detective strategies on EcoRI. More importantly, the convenience and cost make this one-step method quite attractive for application transformation. Therefore, we hope this method could be a hopeful option for EcoRI activity determination, and further to help monitoring the quality of tool enzymes and promote the development of high-through automatic drug screening system.
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Affiliation(s)
- Zhenwei Tang
- School of Life Sciences, Central South University, Changsha 410013, China; Clinical Medicine Eight-year Program, Xiangya Medical School of Central South University, Changsha 410013, China
| | - Haisheng Liu
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Mingjian Chen
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Changbei Ma
- School of Life Sciences, Central South University, Changsha 410013, China.
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5
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Deng J, Walther A. Pathway Complexity in Fuel-Driven DNA Nanostructures with Autonomous Reconfiguration of Multiple Dynamic Steady States. J Am Chem Soc 2020; 142:685-689. [DOI: 10.1021/jacs.9b11598] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jie Deng
- A3BMS Lab, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104 Freiburg, Germany
- DFG Cluster of Excellence “Living, Adaptive and Energy-Autonomous Materials Systems” (livMatS), 79110 Freiburg, Germany
- Freiburg Materials Research Center, University of Freiburg, Stefan-Meier-Straße 21, 79104 Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Andreas Walther
- A3BMS Lab, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104 Freiburg, Germany
- DFG Cluster of Excellence “Living, Adaptive and Energy-Autonomous Materials Systems” (livMatS), 79110 Freiburg, Germany
- Freiburg Materials Research Center, University of Freiburg, Stefan-Meier-Straße 21, 79104 Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
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6
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Nucleic acid-based fluorescent methods for the determination of DNA repair enzyme activities: A review. Anal Chim Acta 2019; 1060:30-44. [DOI: 10.1016/j.aca.2018.12.055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/09/2018] [Accepted: 12/18/2018] [Indexed: 12/13/2022]
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7
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Gulfam M, Sahle FF, Lowe TL. Design strategies for chemical-stimuli-responsive programmable nanotherapeutics. Drug Discov Today 2019; 24:129-147. [PMID: 30292916 PMCID: PMC6372326 DOI: 10.1016/j.drudis.2018.09.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 08/06/2018] [Accepted: 09/26/2018] [Indexed: 02/06/2023]
Abstract
Chemical-stimuli-responsive nanotherapeutics have gained great interest in drug delivery and diagnosis applications. These nanotherapeutics are designed to respond to specific internal stimuli including pH, ionic strength, redox, reactive oxygen species, glucose, enzymes, ATP and hypoxia for site-specific and responsive or triggered release of payloads and/or biomarker detections. This review systematically and comprehensively addresses up-to-date technological and design strategies, and challenges nanomaterials to be used for triggered release and sensing in response to chemical stimuli.
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Affiliation(s)
- Muhammad Gulfam
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Fitsum Feleke Sahle
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Tao L Lowe
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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8
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Fan K, Zheng C, Zhao Y, Fu H, Qu B, Lu L. Label-free ultrasensitive determination of EcoRI activity based on terminal deoxynucleotidyl transferase generated G-quadruplexes. Microchem J 2018. [DOI: 10.1016/j.microc.2018.08.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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9
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Abstract
DNA repair is now understood to play a key role in a variety of disease states, most notably cancer. Tools for studying DNA have typically relied on traditional biochemical methods which are often laborious and indirect. Efforts to study the biology and therapeutic relevance of DNA repair pathways can be limited by such methods. Recently, specific fluorescent probes have been developed to aid in the study of DNA repair. Fluorescent probes offer the advantage of being able to directly assay for DNA repair activity in a simple, mix-and-measure format. This review will summarize the distinct classes of probe designs and their potential utility in varied research and preclinical settings.
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Affiliation(s)
- David L. Wilson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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10
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Demuth J, Kucera R, Kopecky K, Havlínová Z, Libra A, Novakova V, Miletin M, Zimcik P. Efficient Synthesis of a Wide-Range Absorbing Azaphthalocyanine Dark Quencher and Its Application to Dual-Labeled Oligonucleotide Probes for Quantitative Real-Time Polymerase Chain Reactions. Chemistry 2018; 24:9658-9666. [PMID: 29683215 DOI: 10.1002/chem.201801319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Indexed: 11/06/2022]
Abstract
Unsymmetrical dialkylamino-substituted zinc azaphthalocyanine (AzaPc) exhibits unique spectral and photophysical properties for dark quenchers of fluorescence in DNA hybridization probes. The panchromatic light absorption of AzaPc from 300 nm up to at least 700 nm and its lack of fluorescence make it an ideal candidate for a universal dark quencher. To prove this experimentally, oligodeoxyribonucleotide probes were labeled at the 3'-end by this AzaPc and at the 5'-end by a fluorophore used in the polymerase chain reaction (PCR)-that is, fluorescein, CAL Fluor Red 610, and Cy5. AzaPc showed a significantly higher quenching efficiency compared to the commercially available dark quenchers (BHQ-1, BHQ-2, BBQ-650) in a developed model of TaqMan PCR assay. The AzaPc-labeled probe proved to also be useful in a practical PCR assay for the quantification of the SLCO2B1 transporter gene expression. The constructed calibration curves indicated linearity in the range from 102 to 107 of target copies.
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Affiliation(s)
- Jiri Demuth
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Radim Kucera
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Kamil Kopecky
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Zuzana Havlínová
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic.,Generi Biotech, Machkova 587, Hradec Kralove, 500 11, Czech Republic
| | - Antonín Libra
- Generi Biotech, Machkova 587, Hradec Kralove, 500 11, Czech Republic
| | - Veronika Novakova
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Miroslav Miletin
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Petr Zimcik
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
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11
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Si Y, Bai Y, Qin X, Li J, Zhong W, Xiao Z, Li J, Yin Y. Alkyne–DNA-Functionalized Alloyed Au/Ag Nanospheres for Ratiometric Surface-Enhanced Raman Scattering Imaging Assay of Endonuclease Activity in Live Cells. Anal Chem 2018; 90:3898-3905. [DOI: 10.1021/acs.analchem.7b04735] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yanmei Si
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha 410082, China
| | - Yaocai Bai
- Department of Chemistry, University of California—Riverside, Riverside, California 92521, United States
| | - Xiaojie Qin
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha 410082, China
| | - Jun Li
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha 410082, China
| | - Wenwan Zhong
- Department of Chemistry, University of California—Riverside, Riverside, California 92521, United States
| | - Zhijun Xiao
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha 410082, China
| | - Jishan Li
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha 410082, China
| | - Yadong Yin
- Department of Chemistry, University of California—Riverside, Riverside, California 92521, United States
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12
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Guo L, Zhang Z, Tang Y. Cationic conjugated polymers as signal reporter for label-free assay based on targets-mediated aggregation of perylene diimide quencher. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.08.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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13
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Hildebrandt N, Spillmann CM, Algar WR, Pons T, Stewart MH, Oh E, Susumu K, Díaz SA, Delehanty JB, Medintz IL. Energy Transfer with Semiconductor Quantum Dot Bioconjugates: A Versatile Platform for Biosensing, Energy Harvesting, and Other Developing Applications. Chem Rev 2016; 117:536-711. [DOI: 10.1021/acs.chemrev.6b00030] [Citation(s) in RCA: 457] [Impact Index Per Article: 57.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Niko Hildebrandt
- NanoBioPhotonics
Institut d’Electronique Fondamentale (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, 91400 Orsay, France
| | | | - W. Russ Algar
- Department
of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Thomas Pons
- LPEM;
ESPCI Paris, PSL Research University; CNRS; Sorbonne Universités, UPMC, F-75005 Paris, France
| | | | - Eunkeu Oh
- Sotera Defense Solutions, Inc., Columbia, Maryland 21046, United States
| | - Kimihiro Susumu
- Sotera Defense Solutions, Inc., Columbia, Maryland 21046, United States
| | - Sebastian A. Díaz
- American Society for Engineering Education, Washington, DC 20036, United States
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14
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Fluorescent drug screening based on aggregation of DNA-templated silver nanoclusters, and its application to iridium (III) derived anticancer drugs. Mikrochim Acta 2016. [DOI: 10.1007/s00604-016-1775-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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15
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Zhao G, Hu T, Li J, Wei H, Shang H, Guan Y. A RCA-based assay for analyzing individual strand break in DNA heteroduplex cleavage by restriction endonucleases. Chem Commun (Camb) 2015; 50:11930-3. [PMID: 25157639 DOI: 10.1039/c4cc05314a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We have developed a rapid and high-throughput assay based on rolling circle amplification, to distinguish individual strand cleavage of DNA duplexes by restriction endonucleases. As an illustration, we analyzed nicking activity of Nb.BbvCI and uneven cleavage of LNA modified DNA by EcoRI. This assay has potential for analyzing protein-DNA interactions.
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Affiliation(s)
- Guojie Zhao
- Key Laboratory of Medical Cell Biology (Ministry of Education), Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, Liaoning 110001, China.
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16
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Lou J, Liu S, Tu W, Dai Z. Graphene quantums dots combined with endonuclease cleavage and bidentate chelation for highly sensitive electrochemiluminescent DNA biosensing. Anal Chem 2015; 87:1145-51. [PMID: 25523862 DOI: 10.1021/ac5037318] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A novel strategy for highly sensitive electrochemiluminescence (ECL) detection of DNA was proposed based on site-specific cleavage of BamHI endonuclease combined with the excellent ECL activity of graphene quantum dots (GQDs) and bidentate chelation of the dithiocarbamate DNA (DTC-DNA) probe assembly. The difference between photoluminescence and ECL spectral peaks suggested that a negligible defect existed on the GQDs surface for generation of an ECL signal. The formed DTC-DNA was directly attached to the gold surface by bidentate anchoring (S-Au-S bonds), which conferred a strong affinity between the ligands and the gold surface, increasing the robustness of DNA immobilization on the gold surface. BamHI endonuclease site-specifically recognized and cleaved the duplex symmetrical sequence, which made the double-stranded DNA fragments and GQDs break off from the electrode surface, inducing a decrease of the ECL signal. Using hepatitis C virus-1b genotype complementary DNA (HCV-1b cDNA) as a model, a novel signal-off ECL DNA biosensor was developed based on variation of the ECL intensity before and after digestion of the DNA hybrid. Electrochemical impedance spectroscopy confirmed the successful fabrication of the ECL DNA biosensor. This ECL biosensor for HCV-1b cDNA determination exhibited a linear range from 5 fM to 100 pM with a detection limit of 0.45 fM at a signal-to-noise ratio of 3 and showed satisfactory selectivity and good stability, which validated the feasibility of the designed strategy. The proposed strategy may be conveniently combined with other specific biological recognition events for expansion of the biosensing application, especially in clinical diagnoses.
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Affiliation(s)
- Jing Lou
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, College of Chemistry and Materials Science, Nanjing Normal University , Nanjing, 210023, P. R. China
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17
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Xu Q, Zhang Y, Zhang CY. A triple-color fluorescent probe for multiple nuclease assays. Chem Commun (Camb) 2015; 51:9121-4. [DOI: 10.1039/c5cc02177d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We develop a triple-color fluorescent probe which may function as a lab-on-a-DNA-molecule for simultaneous detection of multiple nucleases.
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Affiliation(s)
- Qinfeng Xu
- Single-Molecule Detection and Imaging Laboratory
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
- China
| | - Yihong Zhang
- Single-Molecule Detection and Imaging Laboratory
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
- China
| | - Chun-yang Zhang
- Single-Molecule Detection and Imaging Laboratory
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
- China
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18
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Ma DL, Lu L, Lin S, He B, Leung CH. A G-triplex luminescent switch-on probe for the detection of mung bean nuclease activity. J Mater Chem B 2015; 3:348-352. [DOI: 10.1039/c4tb01569j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A G-triplex luminescent switch-on probe for the detection of nuclease activity.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Lihua Lu
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Sheng Lin
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Bingyong He
- Department of Chemistry
- Hong Kong Baptist University
- Kowloon Tong
- China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Macao
- China
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19
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He X, Ma N. An overview of recent advances in quantum dots for biomedical applications. Colloids Surf B Biointerfaces 2014; 124:118-31. [DOI: 10.1016/j.colsurfb.2014.06.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/23/2014] [Accepted: 06/01/2014] [Indexed: 12/23/2022]
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20
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A versatile biosensing system for DNA-related enzyme activity assay via the synthesis of silver nanoclusters using enzymatically-generated DNA as template. Biosens Bioelectron 2014; 61:321-7. [DOI: 10.1016/j.bios.2014.05.038] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/06/2014] [Accepted: 05/15/2014] [Indexed: 01/24/2023]
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21
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Song C, Zhang Q, Han GM, Du YC, Kong DM. A facile fluorescence method for endonuclease detection using exonuclease III-aided signal amplification of a molecular beacon. RSC Adv 2014. [DOI: 10.1039/c4ra09676b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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22
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Lu L, Shiu-Hin Chan D, Kwong DWJ, He HZ, Leung CH, Ma DL. Detection of nicking endonuclease activity using a G-quadruplex-selective luminescent switch-on probe. Chem Sci 2014. [DOI: 10.1039/c4sc02032d] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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23
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He Y, Jiao B. An ultrasensitive fluorometric platform for S1 nuclease assay based on cytochrome c. RSC Adv 2014. [DOI: 10.1039/c4ra05088f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An ultrasensitive and straightforward fluorescent sensing platform for S1 nuclease activity has been developed based on cytochrome c.
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Affiliation(s)
- Yue He
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing)
- Ministry of Agriculture
- Citrus Research Institute
- Southwest University
- Chongqing, China
| | - Bining Jiao
- Laboratory of Quality & Safety Risk Assessment for Citrus Products (Chongqing)
- Ministry of Agriculture
- Citrus Research Institute
- Southwest University
- Chongqing, China
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24
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A label-free DNA-templated silver nanocluster probe for fluorescence on–off detection of endonuclease activity and inhibition. Biosens Bioelectron 2014; 51:408-12. [DOI: 10.1016/j.bios.2013.07.060] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 07/21/2013] [Accepted: 07/23/2013] [Indexed: 01/03/2023]
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25
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Enzymatic cleavage of type II restriction endonucleases on the 2'-O-methyl nucleotide and phosphorothioate substituted DNA. PLoS One 2013; 8:e79415. [PMID: 24260216 PMCID: PMC3829850 DOI: 10.1371/journal.pone.0079415] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 09/21/2013] [Indexed: 11/19/2022] Open
Abstract
The effects of nucleotide analogue substitution on the cleavage efficiencies of type II restriction endonucleases have been investigated. Six restriction endonucleases (EcoRV, SpeI, XbaI, XhoI, PstI and SphI) were investigated respectively regarding their cleavage when substrates were substituted by 2′-O-methyl nucleotide (2′-OMeN) and phosphorothioate (PS). Substitutions were made in the recognition sequence and the two nucleotides flanking the recognition sequence for each endonuclease. The endonuclease cleavage efficiencies were determined using FRET-based assay. Results demonstrated a position-dependent inhibitory effect of substitution on the cleavage efficiency for all the six endonucleases. In general, the 2′-OMeN substitutions had greater impact than the PS substitutions on the enzymatic activities. Nucleotides of optimal substitutions for protection against RE cleavage were identified. Experimental results and conclusions in this study facilitate our insight into the DNA-protein interactions and the enzymatic cleavage mechanism, particularly for those whose detailed structure information is not available. In addition, the information could benefit the development of bioengineering and synthetic biology.
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26
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Effects of 2'-O-methyl nucleotide substitution on EcoRI endonuclease cleavage activities. PLoS One 2013; 8:e77111. [PMID: 24194862 PMCID: PMC3806743 DOI: 10.1371/journal.pone.0077111] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 08/30/2013] [Indexed: 11/19/2022] Open
Abstract
To investigate the effect of sugar pucker conformation on DNA-protein interactions, we used 2′-O-methyl nucleotide (2′-OMeN) to modify the EcoRI recognition sequence -TGAATTCT-, and monitored the enzymatic cleavage process using FRET method. The 2′-O-methyl nucleotide has a C3′-endo sugar pucker conformation different from the C2′-endo sugar pucker conformation of native DNA nucleotides. The initial reaction velocities were measured and the kinetic parameters, Km and Vmax were derived using Michaelis-Menten equation. Experimental results showed that 2′-OMeN substitutions for the EcoRI recognition sequence decreased the cleavage efficiency for A2, A3 and T4 substitutions significantly, and 2′-OMeN substitution for T5 residue inhibited the enzymatic activity completely. In contrast, substitutions for G1 and C6 could maintain the original activity. 2′-fluoro nucleic acid (2′-FNA) and locked nucleic acid (LNA) having similar C3′-endo sugar pucker conformation also demonstrated similar enzymatic results. This position-dependent enzymatic cleavage property might be attributed to the phosphate backbone distortion caused by the switch from C2′-endo to C3′-endo sugar pucker conformation, and was interpreted on the basis of the DNA-EcoRI structure. These 2′-modified nucleotides could behave as a regulatory element to modulate the enzymatic activity in vitro, and this property will have potential applications in genetic engineering and biomedicine.
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27
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Assaying multiple restriction endonucleases functionalities and inhibitions on DNA microarray with multifunctional gold nanoparticle probes. Biosens Bioelectron 2013; 52:118-23. [PMID: 24035855 DOI: 10.1016/j.bios.2013.08.045] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Revised: 08/13/2013] [Accepted: 08/22/2013] [Indexed: 11/20/2022]
Abstract
Herein, a double-stranded (ds) DNA microarray-based resonance light scattering (RLS) assay with multifunctional gold nanoparticle (GNP) probes has been developed for studying restriction endonuclease functionality and inhibition. Because of decreasing significantly melting temperature, the enzyme-cleaved dsDNAs easily unwind to form single-stranded (ss) DNAs. The ssDNAs are hybridized with multiplex complementary ssDNAs functionalized GNP probes followed by silver enhancement and RLS detection. Three restriction endonucleases (EcoRI, BamHI and EcoRV) and three potential inhibitors (doxorubicin hydrochloride (DOX), ethidium bromide (EB) and an EcoRI-derived helical peptide (α4)) were selected to demonstrate capability of the assay. Enzyme activities of restriction endonucleases are detected simultaneously with high specificity down to the limits of 2.0 × 10(-2)U/mL for EcoRI, 1.1 × 10(-2)U/mL for BamHI and 1.6 × 10(-2)U/mL for EcoRV, respectively. More importantly, the inhibitory potencies of three inhibitors are showed quantitatively, indicating that our approach has great promise for high-throughput screening of restriction endonuclease inhibitors.
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28
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Crew E, Yan H, Lin L, Yin J, Skeete Z, Kotlyar T, Tchah N, Lee J, Bellavia M, Goodshaw I, Joseph P, Luo J, Gal S, Zhong CJ. DNA assembly and enzymatic cutting in solutions: a gold nanoparticle based SERS detection strategy. Analyst 2013; 138:4941-9. [DOI: 10.1039/c3an00683b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Ma L, Su M, Li T, Wang Z. Microarray-based fluorescence assay of endonuclease functionality and inhibition. Analyst 2013; 138:1048-52. [DOI: 10.1039/c2an36638j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Lin L, Crew E, Yan H, Shan S, Skeete Z, Mott D, Krentsel T, Yin J, Chernova NA, Luo J, Engelhard MH, Wang C, Li Q, Zhong CJ. Bifunctional nanoparticles for SERS monitoring and magnetic intervention of assembly and enzyme cutting of DNAs. J Mater Chem B 2013; 1:4320-4330. [DOI: 10.1039/c3tb20446d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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31
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Leung CH, Zhong HJ, He HZ, Lu L, Chan DSH, Ma DL. Luminescent oligonucleotide-based detection of enzymes involved with DNA repair. Chem Sci 2013. [DOI: 10.1039/c3sc51228b] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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32
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Zhang Q, Kong DM. A general fluorescent sensor design strategy for “turn-on” activity detection of exonucleases and restriction endonucleases based on graphene oxide. Analyst 2013; 138:6437-44. [DOI: 10.1039/c3an01447a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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33
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Sun SK, Wang BB, Yan XP. A label-free near-infrared fluorescent assay for the determination of deoxyribonuclease I activity based on malachite green/G-quadruplexes. Analyst 2013; 138:2592-7. [DOI: 10.1039/c3an00213f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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34
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Chen NT, Cheng SH, Liu CP, Souris JS, Chen CT, Mou CY, Lo LW. Recent advances in nanoparticle-based Förster resonance energy transfer for biosensing, molecular imaging and drug release profiling. Int J Mol Sci 2012; 13:16598-623. [PMID: 23443121 PMCID: PMC3546710 DOI: 10.3390/ijms131216598] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 11/15/2012] [Accepted: 11/16/2012] [Indexed: 01/10/2023] Open
Abstract
Förster resonance energy transfer (FRET) may be regarded as a "smart" technology in the design of fluorescence probes for biological sensing and imaging. Recently, a variety of nanoparticles that include quantum dots, gold nanoparticles, polymer, mesoporous silica nanoparticles and upconversion nanoparticles have been employed to modulate FRET. Researchers have developed a number of "visible" and "activatable" FRET probes sensitive to specific changes in the biological environment that are especially attractive from the biomedical point of view. This article reviews recent progress in bringing these nanoparticle-modulated energy transfer schemes to fruition for applications in biosensing, molecular imaging and drug delivery.
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Affiliation(s)
- Nai-Tzu Chen
- Division of Medical Engineering Research, National Health Research Institutes, Zhunan 35053, Miaoli County, Taiwan; E-Mails: (N.-T.C.); (S.-H.C.); (C.-P.L.)
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan; E-Mail:
| | - Shih-Hsun Cheng
- Division of Medical Engineering Research, National Health Research Institutes, Zhunan 35053, Miaoli County, Taiwan; E-Mails: (N.-T.C.); (S.-H.C.); (C.-P.L.)
- Department of Radiology, The University of Chicago, Chicago, IL 60637, USA; E-Mails: (J.S.S.); (C.-T.C.)
| | - Ching-Ping Liu
- Division of Medical Engineering Research, National Health Research Institutes, Zhunan 35053, Miaoli County, Taiwan; E-Mails: (N.-T.C.); (S.-H.C.); (C.-P.L.)
| | - Jeffrey S. Souris
- Department of Radiology, The University of Chicago, Chicago, IL 60637, USA; E-Mails: (J.S.S.); (C.-T.C.)
| | - Chen-Tu Chen
- Department of Radiology, The University of Chicago, Chicago, IL 60637, USA; E-Mails: (J.S.S.); (C.-T.C.)
| | - Chung-Yuan Mou
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan; E-Mail:
| | - Leu-Wei Lo
- Division of Medical Engineering Research, National Health Research Institutes, Zhunan 35053, Miaoli County, Taiwan; E-Mails: (N.-T.C.); (S.-H.C.); (C.-P.L.)
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35
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Tian J, Wang Y, Chen S, Jiang Y, Zhao Y, Zhao S. Mass-amplifying quantum dots in a fluorescence polarization-based aptasensor for ATP. Mikrochim Acta 2012. [DOI: 10.1007/s00604-012-0919-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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36
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Zelzer M, Todd SJ, Hirst AR, McDonald TO, Ulijn RV. Enzyme responsive materials: design strategies and future developments. Biomater Sci 2012; 1:11-39. [PMID: 32481995 DOI: 10.1039/c2bm00041e] [Citation(s) in RCA: 194] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Enzyme responsive materials (ERMs) are a class of stimuli responsive materials with broad application potential in biological settings. This review highlights current and potential future design strategies for ERMs and provides an overview of the present state of the art in the area.
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Affiliation(s)
- Mischa Zelzer
- WestCHEM, Thomas Graham Building, 295 Cathedral Street, Glasgow, G1 1XL, U.K..
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37
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Xue M, Wang X, Duan L, Gao W, Ji L, Tang B. A new nanoprobe based on FRET between functional quantum dots and gold nanoparticles for fluoride anion and its applications for biological imaging. Biosens Bioelectron 2012; 36:168-73. [PMID: 22560439 DOI: 10.1016/j.bios.2012.04.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 04/05/2012] [Accepted: 04/09/2012] [Indexed: 02/02/2023]
Abstract
A new nanoprobe was designed for the fluorescence imaging of fluoride anion (F(-)) in living cells with high sensitivity and selectivity. The design is based on the fluorescence resonance energy transfer (FRET) between CdTe quantum dots (CdTe QDs) and gold nanoparticles (AuNPs) through the formation of cyclic esters between phenylborinic acid and diol. In the presence of F(-), the boronate ester, a "hard acid", strongly reacts with F(-), a "hard base". Therefore, the boronate ester is converted to trifluoro borate, which causes the breakage of the linkage and disassembles CdTe QDs from AuNPs, resulting in the fluorescence recovery of the quenched CdTe QDs. The interaction mechanism was investigated by (19)FNMR on a model that was constructed by a small molecule and F(-). Quantum chemical calculations also testify the reactivity of boronate ester to F(-) and the sensing mechanism. Experimental results show that the increase in fluorescence intensity is proportional to the concentration of F(-) in the range of 5.0-45 μM. The detection limit and the relative standard deviation were 50 nM and 2.6%, respectively. Fluorescence imaging of F(-) in macrophages cells indicates good cell membrane penetration ability and low cytotoxicity of the nanoprobe, providing a viable alternative to detection of F(-) in biological or environmental samples.
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Affiliation(s)
- Mei Xue
- College of Chemistry, Chemical Engineering and Materials Science, Engineering Research Center of Pesticide and Medicine Intermediate Clean Production, Ministry of Education, Shandong Normal University, Jinan, PR China
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38
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Affiliation(s)
- Francis P. Zamborini
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292,
United States
| | - Lanlan Bao
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292,
United States
| | - Radhika Dasari
- Department
of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, United States
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